An Ode to Quantifying Infection Risk in Addition to Prevalence

When you’re studying parasites (or symbionts or pathogens), the prevalence of the parasite in the host population is one of the easiest response variables to measure. That’s not to say that it is easy; there are certainly a variety of methodological difficulties that crop up, and it can be expensive to run lots of blood tests if you’re looking at seroprevalence. But getting a prevalence estimate is certainly a lot easier than pinpointing when each host becomes infected (e.g., via mark-recapture methods) and/or calculating the actual risk of infection (i.e., the rate that susceptible hosts become infected = force of infection). For that reason, we often use prevalence as a response variable, and hope that we can infer things about parasite transmission based on those data. Sometimes, it works out great! For instance, in 1854, John Snow (the physician, not the Brother on the Wall) mapped the locations of Cholera cases in London. By pinpointing an area of high incidence on the map, he found a water pump that was probably an important source of infection in the epidemic. But do areas of high disease incidence or prevalence always occur in areas of high disease exposure?

Littorina littorea, the common periwinkle, is an abundant and widespread marine snail that hangs out in the intertidal zone (various levels of exposure to the air with the tides) and the subtidal zone (almost never exposed to air). Periwinkles are hosts for a few different trematode species, but for today, we’ll just focus on Cryptocotyle lingua, which infects snails, then fish, then shorebirds. Snails get infected when they consume trematode eggs from shorebird feces. ‘Loitering’ shorebirds are 6-20 times more likely to hang out in the high intertidal zone than the low intertidal zone, and as a result, the density of shorebird feces in the high intertidal zone is 70 times higher than in the low intertidal zone (Byers et al. 2015). Therefore, it is not surprising that when uninfected ‘sentinel’ snails were placed in field cages in the high and low intertidal zones, snails were four times more likely to become infected in the high intertidal zone (Byers et al. 2015). In fact, the probability that an uninfected snail would become infected in the low intertidal zone was effectively zero. That makes sense, because bird guano was almost never found in that zone.

So, when Byers et al. (2015) went out and sampled periwinkles in the high and low intertidal zones, they found way higher prevalences of infection in the high intertidal zone, where infection risk was high, right? WRONG! The prevalence of infection was much higher in the low intertidal zone, even though snails do not become infected there! How could that be?

First, let’s back up and talk about an important selection pressure in the low intertidal zone: predation. There are extreme size-dependent predation pressures in that zone that pretty much prevent small/young snails from living there. So, the only snails in the low intertidal zone are bigger/older snails. Big/old snails are much more likely to be infected by trematodes than small/young snails, because they have had longer to be exposed and become infected. But we know that the big snails aren’t becoming infected in the low intertidal zone, so where are they coming from? It may be that young snails hang out in the high intertidal zone, escaping predation but experiencing high infection risk, until they are big enough to safely live in the low intertidal zone. Once big enough, the snails migrate to that low zone, which provides better foraging opportunities, and the high density of big, infected snails results in high prevalences of infection (76% infection!) in an area that has effectively zero risk of infection. Isn’t that neat?!

So, as Byers et al. (2015) point out, “disease risk and prevalence patterns need not be tightly coupled in space.” I think that’s important to remember when we’re deciding what response variables we want to consider in ecological and epidemiological studies.

periwinklemigration

Reference:

Byers, J.E., A.J. Malek, L.E. Quevillon, I. Altman, and C.L. Keogh. Opposing selective pressures decouple pattern and process of parasitic infection over small spatial scale. Oikos.

Unofficial ESA 2015 Parasite Ecology Cartoon Contest

ESA 2015 is just one month away! Last year, I had tons of fun judging a parasite ecology cartoon contest that no one knew they were participating in. I posted the results here. This year, I’m announcing the (technically second annual) Unofficial ESA Parasite Ecology Cartoon Contest.

Here’s how it works: myself and a top secret team of judges will be watching your symbiont-related talks and taking notes on your use of cartoons. Our favorite cartoonist will be awarded an almost entirely worthless prize (i.e., snail mail from yours truly, some publicity for your cool science, and bragging rights for a year). The cartoons don’t need to be funny! We’re just looking for cartoons that help communicate your work to the audience. That being said, anything punny is worth mega bonus points.

My minions and I should be able to make it to the majority of the parasite-related talks, but it’s logistically impossible for us to see them all. If you know you’re going to have some rocking cartoons and you want in on this highly prestigious contest, let me know in the comments or via email and I’ll make a special effort to come to your talk. This is particularly important if you’re in a session that isn’t parasite-themed.

To anticipate some questions:

Will the judges be participating in the contest? No!

Can I use cartoons from this site, if I use proper attribution? Yes!

Can the judges be swayed by offers of free beer or tenure-track faculty positions? No! (Except yes. So much yes.)

Good luck!!

ASP Teaching Parasitology Symposium

Sadly, I’m not going to the American Society of Parasitologists conference this year. I’m bummed, because I’m missing the awesome talks in the Teaching Parasitology Symposium and the Science Outreach in the Classroom and Beyond session. The talks include:

TEACHING PARASITOLOGY WHILE AVOIDING TRANSMISSION AND INFECTING THE NEXT GENERATION.

SCIENCE OUTREACH THROUGH BLOGGING AND PODCASTING.

PARASITOLOGY AND DISEASE ECOLOGY: A POTENTIAL MUTUALISM FOR UNDERGRADUATE EDUCATION?

And because nothing is quite as beautiful as the marriage of math and parasites, my personal favorite:

USING GROSS PARASITES TO SNEAK EVEN GROSSER EQUATIONS INTO THE INTRODUCTORY BIOLOGY CLASSROOM.

If you’re going to ASP 2015 and you’d like to do a guest post about the things you learn from these cool talks, let me know! I’m sure I’m not the only person who would like to live vicariously through you.

S Car Go

Hi, Folks! I’m still traveling for the holidays, so I can’t do a full post this week. But here’s a punny cartoon! (This doesn’t have anything to do with symbionts, unless you count the fact that both snails and caterpillars have many symbionts.)

Also, remember to vote on the best Parasite Ecology cartoon of 2014! So far, no one has voted Gary for Snail President.

SCarGoGet it? 😛

Best Parasite Ecology Cartoon of 2014?

Happy New Year!!

Last year, I let you guys vote on my best parasite ecology cartoon of 2013. The winner was “Social Networking in Lemurs,” a cartoon about this study that painted lice on lemurs to infer lemur contacts.

So, which of my 2014 parasite ecology cartoons was the best? I’m opening up the voting for these candidates:

1. Endless blood meals for $6.95!

wildebeest buffet2. Feel the water on my exoskeleton

cricketconvo2

3. He’s on ‘todes

gigantism

4. Oldest trick in the book

Fecundity Compensation

5. Vote Gary for Snail President

VoteGary

6. Pirate worms!

HMS Crayfish 2

7. Godzilla’s parasitoids

Godzilla2

8. Niche markets

Crabbies

9. Elepunts

antsandelephant

10. I want grand-seedlings!

antacacialongtermfitness

Pick your top three favorites!

Vaccination Coverage and Herd Immunity

I’ve talked about vaccination and herd immunity on this blog before, but I think it’s important for me to emphasize how INCREDIBLY IMPORTANT it is to get vaccinated.  The importance of vaccinating most of the population is usually explained using mathematics, because scientists study the spread of pathogens by using mathematics.  But today, I’m going to try to explain it with cartoons and pictures, instead of math.

herdimmunity1

herdimmunity2

Without explaining the math, I’ll say that there are some “magic numbers” for vaccination.  These numbers are unique to each pathogen/disease.  For instance, for whooping cough, a disease that can make make babies very sick, the “magic number” is between 92 and 94.  That is, 92-94% of people must be vaccinated in order to prevent disease epidemics of whooping cough.  If that magic number – called the herd immunity threshold – is reached, babies are indirectly protected from whooping cough.  If not, you can expect outbreaks of whooping cough.

So, you might be wondering if there will be outbreaks of whooping cough where you live.  Check out this graphic that was published in Scientific American last year.  If your state’s bar is red – that is, if you live anywhere except Nebraska – you can expect epidemics of whooping cough in your state in the near future.  And while it looks like nobody will be seeing Mumps epidemics any time soon, you can expect to see Measles epidemics in many states.

vaccination coverage

At one point, we’d nearly eliminated whooping cough in the United States by vaccinating children with the DTP vaccine.  Here’s a graph from the CDC showing that after we started using the DTP vaccine around 1950, whooping cough (also called pertussis) almost completely disappeared.  But in the past decade or so, the number of cases reported each year has been increasing. That is likely due to a decline in the effectiveness of the newer pertussis vaccine, rather a decline in vaccination coverage.

pertussis

How to Find a Summer Research Internship in Biology

A note to my regular readers: this post isn’t about parasites.  🙂  But you could find a parasite ecology internship using these methods.

I have accrued something like a gazillion hours worth of looking for and applying to summer undergraduate research internships in biology.  This post summarizes my experience.  I hope someone somewhere finds it useful.  If anyone has any good resources that I haven’t included here, please post them in the comments or email them to me so that I can add them.

Why should you apply for summer research internships?

If you want to go to graduate school and/or have a career in research, participating in summer research internships will be the best form of education that you get as an undergraduate.  Your classes will give you an important foundation of scientific knowledge, but classes rarely teach you to think like a scientist.  You need to learn how to read scientific literature, come up with good scientific questions, design and conduct experiments that can answer your questions, and present your results.  Summer research internships will let you work on those skills full-time for 8-12 weeks.

In addition to being spectacular training, summer research internships can help you get the career opportunities that you want.  First, internships look good on your resume or curriculum vitae.  Going to graduate school with no prior research experience is really hard – you suddenly need to come up with a testable research question and a research plan for the next 2-7 years with no prior experience. (I’m not saying that you can’t do it.  I’m just saying that it’s hard.)  Because graduate advisors know how hard it is for students to successfully deal with that sudden pressure, they prefer to take on students with some prior research experience.  Second, summer research internships almost always involve working very closely with a research mentor, typically a science professor.  That mentor will probably get to know you over the course of the summer better than any of your other professors, and that means they will be able to write you a detailed, personalized letter of recommendation.  A recommendation letter like that is invaluable for applications to grad school, jobs, fellowships, other internships, etc.

Finally, I will mention some other perks:  (1)  IT’S FUN!  When you start looking for internships, you’ll see that you can get paid to go do some amazing things.  Travel internationally!  Travel nationally!  Play in the mud!  Catch bugs!  Work with billion dollar science equipment!  Or whatever else floats your boat.  (2) As I’ll discuss below, not all summer internships pay you, and not all of the internships that pay you will actually pay enough for you to pay your bills.  However, some internships will pay you very well – better than you’d get flipping burgers full time at minimum wage. (3) Summer science internships sure beat flipping burgers full time at minimum wage.

When do you apply?

Typically, applications are due somewhere between January and April.  (This will vary among internship programs.)  However, you should find and apply for internships well in advance of the deadlines.  This is important because many internship applications require letters of recommendation, and you want to give your letter writers plenty of advanced warning.  (Minimum of two weeks, but that’s pushing it.)

How many internships should you apply for?

As many as you can!  The first year that I applied for internships as an undergraduate, I applied for five different internships, and I was accepted for one.  The second year, I applied for ~40 internships and I was again accepted for just one.  (That one turned out to be my dream job, and it totally changed my career plans.)  This is anecdotal evidence, of course, but my point is that applying can be hit or miss.  There is often stiff competition for the best internship opportunities, and mentors need to turn down good applications all the time.  If you can spread your eggs among many baskets, you should.  But don’t try to apply to so many internships that your applications end up being poor quality.

Types of internships:

I’m going to talk more about the different types of internships below when I tell you how to find good internships.  But in general, your best training for graduate school will be internships that center around doing an independent research project.  You typically find these in two flavors: big research programs and smaller, one-professor programs.  In bigger summer research programs, like many REU programs, individual interns are mentored by different individual mentors and there is often a lot of interaction among students.  Summer research programs often include professional development seminars, social events, etc.  There are also internships where it is just one mentor who may have one or many interns.  (There may be professional development seminars, social events, etc. associated with those types of internships, too.)  The main point is to make sure you’d be conducting independent research.

Other internships tend to be more focused on helping out with research activities rather than having an independent project.  This is kind of a fuzzy line.  Helping with other peoples’ projects is a really great way to learn skills and build relationships, and you’ll probably do some helping out no matter what internship you get.  However, exclusively helping is suboptimal if you want a research career.  Some examples would be ‘research assistant’ positions where you help with data collection or enter data into spreadsheets.  These are often advertised as volunteer opportunities.  (Confusingly, not all ‘research assistant’ positions work like that.)  Another example is positions at zoos or other wildlife facilities where you mostly help with cleaning and feeding animals, but you don’t really do any science.  Obviously, those internship opportunities are great if you want to go into medicine or wildlife conservation, but they aren’t good research experiences.

Paid, Partially Paid, or Volunteer?

For many undergraduates, funding is the major barrier for participating in a summer research internship.  You need to get paid enough to pay rent, buy food and gas, and save up to pay for the next year’s tuition.  You might be thinking that no summer research internship is going to pay you enough for all that.  You might be surprised!  The going stipend rate for many NSF REU internships is ~$6000/10 weeks.  That’s probably better than you’ll get paid working full-time for any entry-level-type job for an entire summer (13-16 weeks).  NSF works hard to make the stipends competitive with non-science summer positions so that students from disadvantaged socioeconomic backgrounds can consider science internships as a feasible option.  I will say that if you’re used to working multiple jobs and getting >40 hours/week of work, you won’t be able to do that with an internship.  Most internships have a strict rule that you can’t take on a second job during your tenure.  But you might be able to mow grass or walk dogs or babysit before/after the internship in the remaining summer weeks to make some extra cash.

If you’re financially secure enough that getting paid isn’t particularly important to you, then you have even more internship options!  This especially opens up research assistant positions.  I frequently see advertisements (on ECOLOG, see below) for partially paid and volunteer positions looking for students who want to say, go to Madagascar and help  a graduate student or postdoc study primates.  These often provide housing and meals at the field site, but you have to pay for travel and there isn’t a stipend. Please do not feel pressured to take volunteer positions, especially if taking them jeopardizes your mental or physical well-being via economic hardship. A trusted mentor or professor can help you decide whether an unpaid internship is a good idea.

To travel or not to travel?

In my experience, another big barrier for undergraduates who want to participate in summer research internships is the travel component.  One part of that barrier is money.  Traveling to and from the location of the internship can be costly, and not everyone can afford to take on that cost.  However, many internships pay for the cost of travel – the best example being NSF REU’s (see below).

Travel also involves a whole suite of things that students might find difficult or impossible.  You have to leave your family and friends for months.  You might need to find temporary housing (i.e., a summer sublet) at the internship location.  Maybe you need to find that housing and a roommate without ever seeing the place or roommate in person (thank goodness for Craigslist).  You might need to pay rent for two places all summer, unless you manage to sublet the place you aren’t using while you’re gone (a whole extra headache).  If you have pets, you might not be able to take them with you.  If you’re a nontraditional undergraduate – married?  kids? – uprooting may not be an option, even for the summer.  The list goes on and on.

My advice to you is that if you can travel, you should.  If you can travel but you’d rather not because it’s scary, I’d urge you to try.  First, your internship options will increase dramatically if you aren’t limited to a single geographic area.  Second, meeting new people and trying new things is good for you.  This is probably the best time in your life for you to have some adventures.

For those of you who are thinking, “I love traveling!  Sign me up!”:  keep reading!  Though it was a struggle for me to handle the funding and pet-leaving, I had both national and international internships, and I know that you can, too.

How do you find internships?

Ok, so, finally, how do you find internships to apply to?  I’m going to give you a bunch of good resources, all of which have their strengths and weaknesses:

Your Home Institution:

Most institutions have some kind of summer internship program.  You might ask your academic advisor about this or google “summer biology internship at [your institution].”  Often, institutions have programs called SURF, for Summer Undergraduate Research Fellowship.  You can find those by googling “[your institution] SURF” or something similar.

The NSF REU Website:

The National Science Foundation funds many internships around the United States.  These internships are all called Research Experience for Undergraduates, or REUs.  NSF keeps an online list of most of the REU programs that you can apply to.  They break down the options by discipline on this page, and if you click through to biology you can get the full biology listing.  On the former page there is also a search box, so that you can look for REUs by subject or state or university.  This NSF resource is not always up-to-date.  You might click through to a program that is no longer funded.  In that case, it typically has a note about how the program is not accepting applications this year.  Most pages give you information about potential faculty mentors, provide an application deadline, and explain how to apply.

ECOLOG:

ECOLOG is a listserv for posting and viewing job ads (and other things) that are of interest to ecologists.  You can sign up to receive emails from the listserv here.  This listserv will be your best friend both when you’re looking for summer internship positions and when you’re looking for grad school positions in ecology.  If you’re just joining ECOLOG now, you can look in the archives for REU posts that you might have missed recently.   Note: even if it is tempting, do not post to the listserv asking if anyone has an open position and wants to hire you.  Only use the listserv to look for postings. 

List from the Department of Biology at Columbia University:

Sometimes people put up amazing lists of internship opportunities on the web.  This is one of those lists.  It contains internships that provide you with independent research experience and those that are more volunteer or assistant-type positions.  Many of the links are out of date, but it’s still a great resource.

List from R.I.T.

This is another one of those awesome lists.  You can click through to the list for ecology, plant biology, and marine science.  The things updated for 2013 are highlighted with red 2013 labels.  Some of the other sites may still be active, too, so it’s worth clicking through to check if something seems particularly interesting.

Google:

If you are currently an undergraduate, you are probably very skilled at using The Google.  There are some very good internships just waiting to be found.  Try things like “summer biology internship 2014” and “paid biology internship 2014.”  This can be an especially good way to find international internships, because those don’t always show up in the above resources.  Be careful of scams!

How do you apply for internships?

One thing that I am not going to cover in this post is application tips, except to say that you should always look through the website of the faculty member that you’re interested in and try to read some of their papers, if you can.  Your academic advisor, a helpful professor or mentor, or someone at the career advising center at your university should be able to help you figure out how to write a resume or CV, how to write a cover letter, and how to get a copy of your transcripts.

Good luck!!